useDynLib(caret)
import(lattice)
importFrom(stats, prcomp)

export(anovaScores,
       aucRoc,
       avNNet,
       avNNet.default,
       bag,
       bag.default,
       bagControl,
       bagEarth,
       bagEarth.default,
       bagEarth.formula,
       bagFDA,
       bagFDA.default,
       bagFDA.formula,
       best,
       BoxCoxTrans,
       caretFuncs,
       caretSBF,
       caretTheme,
       checkConditionalX,
       checkResamples,
       classDist,
       classDist.default,
       confusionMatrix,
       confusionMatrix.train,
       contr.dummy,
       createDataPartition,
       createFolds,
       createGrid,
       createModel,
       createMultiFolds,
       createResample,
       ctreeBag,
       defaultSummary,
       densityplot.rfe,
       densityplot.train,
       dotPlot,
       dummyVars,
       dummyVars.default,
       extractPrediction,
       extractProb,
       featurePlot,
       filterVarImp,
       findCorrelation,
       findLinearCombos,
       gamFuncs,
       gamScores,
       generateExprVal.method.trimMean,
       histogram.rfe,
       icr,
       icr.default,
       icr.formula,
       knn3,
       knn3.formula,
       knn3.matrix,
       knn3Train,
       knnreg,
       knnreg.data.frame,
       knnreg.default,
       knnreg.matrix,
       knnregTrain,
       ldaBag,
       ldaFuncs,
       ldaSBF,
       lift,
       lmFuncs,
       lmSBF,
       maxDissim,
       minDiss,
       modelLookup,
       nbBag,
       nbFuncs,
       nbSBF,
       nearZeroVar,
       negPredValue,
       negPredValue.default,
       negPredValue.table,
       nnetBag,
       normalize.AffyBatch.normalize2Reference,
       normalize2Reference,
       nullModel,
       nullModel.default,
       oneSE,
       panel.lift,
       panel.lift2,
       panel.needle,
       parallel.resamples,
       pcaNNet,
       pcaNNet.default,
       pickSizeBest,
       pickSizeTolerance,
       pickVars,
       plot.train,
       plotClassProbs,
       plotObsVsPred,
       plsBag,
       plsda,
       plsda.default,
       posPredValue,
       posPredValue.default,
       posPredValue.table,
       postResample,
       predict.avNNet,
       predict.bag,
       predict.bagEarth,
       predict.bagFDA,
       predict.classDist,
       predict.dummyVars,
       predict.icr,
       predict.knn3,
       predict.knnreg,
       predict.list,
       predict.nullModel,
       predict.pcaNNet,
       predict.plsda,
       predict.preProcess,
       predict.splsda,
       predict.train,
       predictors,
       preProcess,
       preProcess.default,
       print.train,
       R2,
       resampleHist,
       resamples,
       resamples.default,
       resampleSummary,
       resampleWrapper,
       rfe,
       rfe.default,
       rfeControl,
       rfeIter,
       rfFuncs,
       rfSBF,
       RMSE,
       roc,
       sbf,
       sbf.default,
       sbf.formula,
       sbfControl,
       sensitivity,
       sensitivity.default,
       sensitivity.table,
       sortImp,
       spatialSign,
       spatialSign.data.frame,
       spatialSign.default,
       spatialSign.matrix,
       specificity,
       specificity.default,
       specificity.table,
       splsda,
       splsda.default,
       stripplot.rfe,
       sumDiss,
       summary.bagEarth,
       summary.bagFDA,
       svmBag,
       tolerance,
       train,
       train.default,
       train.formula,
       trainControl,
       treebagFuncs,
       treebagSBF,
       twoClassSummary,
       varImp,
       varImp.bagEarth,
       xyplot.rfe
       )

S3method(confusionMatrix, default)
S3method(confusionMatrix, train)
S3method(spatialSign,     default)
S3method(enumLC,          default)
S3method(train,           default)
S3method(PLS,             default)
S3method(plsda,           default)
S3method(splsda,          default)
S3method(bagEarth,        default)
S3method(bagFDA,          default)
S3method(preProcess,      default)
S3method(pcaNNet,         default)
S3method(avNNet,          default)
S3method(sensitivity,     default)
S3method(specificity,     default)
S3method(posPredValue,    default)
S3method(negPredValue,    default)
S3method(rfe,             default)
S3method(classDist,       default)
S3method(knnreg,          default)
S3method(sbf,             default)
S3method(nullModel,       default)
S3method(resamples,       default)
S3method(icr,             default)
S3method(bag,             default)
S3method(dummyVars,       default)
S3method(BoxCoxTrans,     default)


S3method(train,   formula)
S3method(pcaNNet, formula)
S3method(avNNet,  formula)
S3method(rfe,     formula)
S3method(knnreg,  formula)
S3method(sbf,     formula)
S3method(icr,     formula)

S3method(varImp, train)
S3method(varImp, rpart)
S3method(varImp, randomForest)
S3method(varImp, gbm)
S3method(varImp, classbagg)
S3method(varImp, regbagg)
S3method(varImp, pamrtrained)
S3method(varImp, lm)
S3method(varImp, mvr)
S3method(varImp, earth)
S3method(varImp, bagEarth)
S3method(varImp, RandomForest)
S3method(varImp, rfe)
S3method(varImp, sbf)
S3method(varImp, dsa)
S3method(varImp, plsda)
S3method(varImp, fda)
S3method(varImp, multinom)
S3method(varImp, gam)
S3method(varImp, cubist)

S3method(densityplot, train)
S3method(histogram,   train)
S3method(stripplot,   train)
S3method(xyplot,      train)

S3method(densityplot, rfe)
S3method(histogram,   rfe)
S3method(stripplot,   rfe)
S3method(xyplot,      rfe)

S3method(densityplot, sbf)
S3method(histogram,   sbf)

S3method(densityplot, resamples)
S3method(bwplot,      resamples)
S3method(dotplot,     resamples)
S3method(splom,       resamples)
S3method(xyplot,      resamples)
S3method(parallel,    resamples)
S3method(prcomp,      resamples)
S3method(cluster,     resamples)

S3method(densityplot, diff.resamples)
S3method(bwplot,      diff.resamples)
S3method(levelplot,   diff.resamples)
S3method(dotplot,     diff.resamples)

S3method(plot,  train)
S3method(plot,  varImp.train)
S3method(plot,  rfe)
S3method(plot,  prcomp.resamples)

S3method(confusionMatrix,  train)
S3method(confusionMatrix,  rfe)
S3method(confusionMatrix,  sbf)

S3method(print, train)
S3method(print, varImp.train)
S3method(print, confusionMatrix)
S3method(print, confusionMatrix.train)
S3method(print, confusionMatrix.rfe)
S3method(print, confusionMatrix.sbf)
S3method(print, knn3)
S3method(print, plsda)
S3method(print, splsda)
S3method(print, bagEarth)
S3method(print, bagFDA)
S3method(print, summary.bagEarth)
S3method(print, summary.bagFDA)
S3method(print, preProcess)
S3method(print, pcaNNet)
S3method(print, avNNet)
S3method(print, rfe)
S3method(print, classDist)
S3method(print, knnreg)
S3method(print, sbf)
S3method(print, nullModel)
S3method(print, resamples)
S3method(print, summary.resamples)
S3method(print, diff.resamples)
S3method(print, summary.diff.resamples)
S3method(print, icr)
S3method(print, bag)
S3method(print, prcomp.resamples)
S3method(print, dummyVars)
S3method(print, BoxCoxTrans)

S3method(predict, PLS)
S3method(predict, plsda)
S3method(predict, splsda)
S3method(predict, knn3)
S3method(predict, bagEarth)
S3method(predict, bagFDA)
S3method(predict, preProcess)
S3method(predict, pcaNNet)
S3method(predict, avNNet)
S3method(predict, list)
S3method(predict, train)
S3method(predict, classDist)
S3method(predict, knnreg)
S3method(predict, nullModel)
S3method(predict, sbf)
S3method(predict, icr)
S3method(predict, bag)
S3method(predict, rfe)
S3method(predict, dummyVars)
S3method(predict, BoxCoxTrans)

S3method(summary, bagEarth)
S3method(summary, bagFDA)

S3method(format, bagEarth)

S3method(predictors, train)
S3method(predictors, terms)
S3method(predictors, formula)
S3method(predictors, list)
S3method(predictors, mvr)
S3method(predictors, gbm)
S3method(predictors, Weka_classifier)
S3method(predictors, fda)
S3method(predictors, earth)
S3method(predictors, gausspr)
S3method(predictors, ksvm)
S3method(predictors, rvm)
S3method(predictors, lssvm)
S3method(predictors, gpls)
S3method(predictors, knn3)
S3method(predictors, knnreg)
S3method(predictors, LogitBoost)
S3method(predictors, lda)
S3method(predictors, rda)
S3method(predictors, multinom)
S3method(predictors, NaiveBayes)
S3method(predictors, pamrtrained)
S3method(predictors, superpc)
S3method(predictors, randomForest)
S3method(predictors, slda)
S3method(predictors, rpart)
S3method(predictors, regbagg)
S3method(predictors, classbagg)
S3method(predictors, lm)
S3method(predictors, glmboost)
S3method(predictors, blackboost)
S3method(predictors, gamboost)
S3method(predictors, BinaryTree)
S3method(predictors, RandomForest)
S3method(predictors, bagEarth)
S3method(predictors, bagFDA)
S3method(predictors, nnet)
S3method(predictors, pcaNNet)
S3method(predictors, avNNet)
S3method(predictors, rfe)
S3method(predictors, spls)
S3method(predictors, splsda)
S3method(predictors, glm)
S3method(predictors, mda)
S3method(predictors, glmnet)
S3method(predictors, qda)
S3method(predictors, penfit)
S3method(predictors, lars)
S3method(predictors, sda)
S3method(predictors, smda)
S3method(predictors, sbf)
S3method(predictors, trocc)
S3method(predictors, foba)
S3method(predictors, dsa)
S3method(predictors, logreg)
S3method(predictors, logforest)
S3method(predictors, logicBagg)
S3method(predictors, gam)

S3method(confusionMatrix, table)

S3method(sensitivity, table)
S3method(specificity, table)

S3method(posPredValue,    table)
S3method(negPredValue,    table)

S3method(posPredValue,    matrix)
S3method(negPredValue,    matrix)

S3method(as.table,  confusionMatrix)
S3method(as.matrix, confusionMatrix)

S3method(summary, resamples)
S3method(summary, bag)

S3method(diff, resamples)

S3method(summary, diff.resamples)